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Fulltext Habitat modeling of Irrawaddy dolphins (Orcaella brevirostris) in the Eastern Gulf of Thailand

Jackson-Ricketts J, Junchompoo C, Hines EM, Hazen EL, Ponnampalam LS, Ilangakoon A, et al.

Ecol Evol, 2020 Mar;10(6):2778-2792.
PMID: 32211155 DOI: 10.1002/ece3.6023

AIM: The Irrawaddy dolphin (Orcaella brevirostris) is an endangered cetacean found throughout Southeast Asia. The main threat to this species is human encroachment, led by entanglement in fishing gear. Information on this data-poor species' ecology and habitat use is needed to effectively inform spatial management.
LOCATION: We investigated the habitat of a previously unstudied group of Irrawaddy dolphins in the eastern Gulf of Thailand, between the villages of Laem Klat and Khlong Yai, in Trat Province. This location is important as government groups plan to establish a marine protected area.
METHODS: We carried out boat-based visual line transect surveys with concurrent oceanographic measurements and used hurdle models to evaluate this species' patterns of habitat use in this area.
RESULTS: Depth most strongly predicted dolphin presence, while temperature was a strong predictor of group size. The highest probability of dolphin presence occurred at around 10.0 m with an optimal depth range of 7.50 to 13.05 m. The greatest number of dolphins was predicted at 24.93°C with an optimal range between 24.93 and 25.31°C. Dolphins are most likely to occur in two primary locations, one large region in the center of the study area (11o54'18''N to 11o59'23''N) and a smaller region in the south (11o47'28''N to 11o49'59''N). Protections for this population will likely have the greatest chance of success in these two areas.
MAIN CONCLUSIONS: The results of this work can inform management strategies within the immediate study area by highlighting areas of high habitat use that should be considered for marine spatial planning measures, such as the creation of marine protected areas. Species distribution models for this species in Thailand can also assist conservation planning in other parts of the species' range by expanding our understanding of habitat preferences.
Fulltext Molecular sex identification of Malaysian White-Nest Swiftlet (Aerodramus fuciphagus Thunberg, 1812)

Osman MA, Sugnaseelan S, Panandam JM, Ab Ghani NI

Ecol Evol, 2020 Oct;10(19):10440-10448.
PMID: 33072271 DOI: 10.1002/ece3.6699

The difficulty in differentiating the sex of monomorphic bird species has made molecular sexing an important tool in addressing this problem. This method uses noninvasively collected materials such as feathers and may be advantageous for sexing endangered as well as commercialized bird species. In this study, seven primer sets for sexing birds were screened in Aerodramus fuciphagus using a total of 13 feather samples that were randomly selected from the state of Perak, Malaysia. From the screening analysis, only one primer set (P8/WZ/W) successfully differentiated the sex of A. fuciphagus. PCR amplification produced a single 255-bp DNA fragment for males which was derived from CHD-Z (CHD gene region in the sex chromosome Z), while for the females it produced two fragments (144 and 255 bp). The 144-bp fragment was from CHD-W (CHD gene region in the sex chromosome W). Results from sequencing showed no variations in the base sequences of the CHD-W and CHD-Z amplified fragments within the same sexes, except for one male sample (A23) where at position 166, a base substitution occurred (G → A). Phylogenetic analysis of CHD-W showed that four (Apodiformes; Gruiformes; Passeriformes; and Pelecaniformes) out of the five orders investigated had formed four clear clusters within their orders, including the studied order: Apodiformes. Whereas in CHD-Z, four (Accipitriformes; Columbiformes; Galliformes; and Passeriformes) out of five orders investigated formed four clear clusters within their orders, excluding the studied order. In addition, A. fuciphagus and Apus apus (both Apodiformes) showed less divergence in CHD-W than CHD-Z (0% c.f. 9%). The result suggests that in A. fuciphagus, CHD gene evolution occurred at a higher rate in males (CHD-Z) compared to females (CHD-W). This finding may be useful for further studies on sex ratio and breeding management of A. fuciphagus.
Fulltext Making the most of your pollinators: An epiphytic fig tree encourages its pollinators to roam between figs

Mohd Hatta SK, Quinnell RJ, Idris AG, Compton SG

Ecol Evol, 2021 Jun;11(11):6371-6380.
PMID: 34141224 DOI: 10.1002/ece3.7488

Ficus species are characterized by their unusual enclosed inflorescences (figs) and their relationship with obligate pollinator fig wasps (Agaonidae). Fig trees have a variety of growth forms, but true epiphytes are rare, and one example is Ficus deltoidea of Southeast Asia. Presumably as an adaptation to epiphytism, inflorescence design in this species is exceptional, with very few flowers in female (seed-producing) figs and unusually large seeds. Figs on male (pollinator offspring-generating) trees have many more flowers. Many fig wasps pollinate one fig each, but because of the low number of flowers per fig, efficient utilization by F. deltoidea's pollinators depends on pollinators entering several female figs. We hypothesized that it is in the interest of the plants to allow pollinators to re-emerge from figs on both male and female trees and that selection favors pollinator roaming because it increases their own reproductive success. Our manipulations of Blastophaga sp. pollinators in a Malaysian oil palm plantation confirmed that individual pollinators do routinely enter several figs of both sexes. Entering additional figs generated more seeds per pollinator on female trees and more pollinator offspring on male trees. Offspring sex ratios in subsequently entered figs were often less female-biased than in the first figs they entered, which reduced their immediate value to male trees because only female offspring carry their pollen. Small numbers of large seeds in female figs of epiphytic F. deltoidea may reflect constraints on overall female fig size, because pollinator exploitation depends on mutual mimicry between male and female figs.
Fulltext A trait-based trade-off between growth and mortality: evidence from 15 tropical tree species using size-specific relative growth rates

Philipson CD, Dent DH, O'Brien MJ, Chamagne J, Dzulkifli D, Nilus R, et al.

Ecol Evol, 2014 Sep;4(18):3675-88.
PMID: 25478157 DOI: 10.1002/ece3.1186

A life-history trade-off between low mortality in the dark and rapid growth in the light is one of the most widely accepted mechanisms underlying plant ecological strategies in tropical forests. Differences in plant functional traits are thought to underlie these distinct ecological strategies; however, very few studies have shown relationships between functional traits and demographic rates within a functional group. We present 8 years of growth and mortality data from saplings of 15 species of Dipterocarpaceae planted into logged-over forest in Malaysian Borneo, and the relationships between these demographic rates and four key functional traits: wood density, specific leaf area (SLA), seed mass, and leaf C:N ratio. Species-specific differences in growth rates were separated from seedling size effects by fitting nonlinear mixed-effects models, to repeated measurements taken on individuals at multiple time points. Mortality data were analyzed using binary logistic regressions in a mixed-effects models framework. Growth increased and mortality decreased with increasing light availability. Species differed in both their growth and mortality rates, yet there was little evidence for a statistical interaction between species and light for either response. There was a positive relationship between growth rate and the predicted probability of mortality regardless of light environment, suggesting that this relationship may be driven by a general trade-off between traits that maximize growth and traits that minimize mortality, rather than through differential species responses to light. Our results indicate that wood density is an important trait that indicates both the ability of species to grow and resistance to mortality, but no other trait was correlated with either growth or mortality. Therefore, the growth mortality trade-off among species of dipterocarp appears to be general in being independent of species crossovers in performance in different light environments.
Fulltext Predicting dispersal of auto-gyrating fruit in tropical trees: a case study from the Dipterocarpaceae

Smith JR, Bagchi R, Ellens J, Kettle CJ, Burslem DF, Maycock CR, et al.

Ecol Evol, 2015 May;5(9):1794-801.
PMID: 26140196 DOI: 10.1002/ece3.1469

Seed dispersal governs the distribution of plant propagules in the landscape and hence forms the template on which density-dependent processes act. Dispersal is therefore a vital component of many species coexistence and forest dynamics models and is of applied value in understanding forest regeneration. Research on the processes that facilitate forest regeneration and restoration is given further weight in the context of widespread loss and degradation of tropical forests, and provides impetus to improve estimates of seed dispersal for tropical forest trees. South-East Asian lowland rainforests, which have been subject to severe degradation, are dominated by trees of the Dipterocarpaceae family which constitute over 40% of forest biomass. Dipterocarp dispersal is generally considered to be poor given their large, gyration-dispersed fruits. However, there is wide variability in fruit size and morphology which we hypothesize mechanistically underpins dispersal potential through the lift provided to seeds mediated by the wings. We explored experimentally how the ratio of fruit wing area to mass ("inverse wing loading," IWL) explains variation in seed dispersal kernels among 13 dipterocarp species by releasing fruit from a canopy tower. Horizontal seed dispersal distances increased with IWL, especially at high wind speeds. Seed dispersal of all species was predominantly local, with 90% of seed dispersing <10 m, although maximum dispersal distances varied widely among species. We present a generic seed dispersal model for dipterocarps based on attributes of seed morphology and provide modeled seed dispersal kernels for all dipterocarp species with IWLs of 1-50, representing 75% of species in Borneo.
Fulltext A comparative analysis reveals weak relationships between ecological factors and beta diversity of stream insect metacommunities at two spatial levels

Heino J, Melo AS, Bini LM, Altermatt F, Al-Shami SA, Angeler DG, et al.

Ecol Evol, 2015 Mar;5(6):1235-48.
PMID: 25859329 DOI: 10.1002/ece3.1439

The hypotheses that beta diversity should increase with decreasing latitude and increase with spatial extent of a region have rarely been tested based on a comparative analysis of multiple datasets, and no such study has focused on stream insects. We first assessed how well variability in beta diversity of stream insect metacommunities is predicted by insect group, latitude, spatial extent, altitudinal range, and dataset properties across multiple drainage basins throughout the world. Second, we assessed the relative roles of environmental and spatial factors in driving variation in assemblage composition within each drainage basin. Our analyses were based on a dataset of 95 stream insect metacommunities from 31 drainage basins distributed around the world. We used dissimilarity-based indices to quantify beta diversity for each metacommunity and, subsequently, regressed beta diversity on insect group, latitude, spatial extent, altitudinal range, and dataset properties (e.g., number of sites and percentage of presences). Within each metacommunity, we used a combination of spatial eigenfunction analyses and partial redundancy analysis to partition variation in assemblage structure into environmental, shared, spatial, and unexplained fractions. We found that dataset properties were more important predictors of beta diversity than ecological and geographical factors across multiple drainage basins. In the within-basin analyses, environmental and spatial variables were generally poor predictors of variation in assemblage composition. Our results revealed deviation from general biodiversity patterns because beta diversity did not show the expected decreasing trend with latitude. Our results also call for reconsideration of just how predictable stream assemblages are along ecological gradients, with implications for environmental assessment and conservation decisions. Our findings may also be applicable to other dynamic systems where predictability is low.
Fulltext The PREDICTS database: a global database of how local terrestrial biodiversity responds to human impacts

Hudson LN, Newbold T, Contu S, Hill SL, Lysenko I, De Palma A, et al.

Ecol Evol, 2014 Dec;4(24):4701-35.
PMID: 25558364 DOI: 10.1002/ece3.1303

Biodiversity continues to decline in the face of increasing anthropogenic pressures such as habitat destruction, exploitation, pollution and introduction of alien species. Existing global databases of species' threat status or population time series are dominated by charismatic species. The collation of datasets with broad taxonomic and biogeographic extents, and that support computation of a range of biodiversity indicators, is necessary to enable better understanding of historical declines and to project - and avert - future declines. We describe and assess a new database of more than 1.6 million samples from 78 countries representing over 28,000 species, collated from existing spatial comparisons of local-scale biodiversity exposed to different intensities and types of anthropogenic pressures, from terrestrial sites around the world. The database contains measurements taken in 208 (of 814) ecoregions, 13 (of 14) biomes, 25 (of 35) biodiversity hotspots and 16 (of 17) megadiverse countries. The database contains more than 1% of the total number of all species described, and more than 1% of the described species within many taxonomic groups - including flowering plants, gymnosperms, birds, mammals, reptiles, amphibians, beetles, lepidopterans and hymenopterans. The dataset, which is still being added to, is therefore already considerably larger and more representative than those used by previous quantitative models of biodiversity trends and responses. The database is being assembled as part of the PREDICTS project (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems - http://www.predicts.org.uk). We make site-level summary data available alongside this article. The full database will be publicly available in 2015.
Fulltext First mitogenome phylogeny of the sun bear Helarctos malayanus reveals a deep split between Indochinese and Sundaic lineages

Kunde MN, Barlow A, Klittich AM, Yakupova A, Patel RP, Fickel J, et al.

Ecol Evol, 2023 Apr;13(4):e9969.
PMID: 37082317 DOI: 10.1002/ece3.9969

The sun bear Helarctos malayanus is one of the most endangered ursids, and to date classification of sun bear populations has been based almost exclusively on geographic distribution and morphology. The very few molecular studies focussing on this species were limited in geographic scope. Using archival and non-invasively collected sample material, we have added a substantial number of complete or near-complete mitochondrial genome sequences from sun bears of several range countries of the species' distribution. We here report 32 new mitogenome sequences representing sun bears from Cambodia, Thailand, Peninsular Malaysia, Sumatra, and Borneo. Reconstruction of phylogenetic relationships revealed two matrilines that diverged ~295 thousand years ago: one restricted to portions of mainland Indochina (China, Cambodia, Thailand; "Mainland clade"), and one comprising bears from Borneo, Sumatra, Peninsular Malaysia but also Thailand ("Sunda clade"). Generally recent coalescence times in the mitochondrial phylogeny suggest that recent or historical demographic processes have resulted in a loss of mtDNA variation. Additionally, analysis of our data in conjunction with shorter mtDNA sequences revealed that the Bornean sun bear, classified as a distinct subspecies (H. m. euryspilus), does not harbor a distinctive matriline. Further molecular studies of H. malayanus are needed, which should ideally include data from nuclear loci.
Fulltext Digitization of natural history collections: A guideline and nationwide capacity building workshop in Malaysia

Ong SQ, Mat Jalaluddin NS, Yong KT, Ong SP, Lim KF, Azhar S

Ecol Evol, 2023 Jun;13(6):e10212.
PMID: 37325726 DOI: 10.1002/ece3.10212

Natural history museum collections are the most important sources of information on the present and past biodiversity of our planet. Most of the information is primarily stored in analogue form, and digitization of the collections can provide further open access to the images and specimen data to address the many global challenges. However, many museums do not digitize their collections because of constraints on budgets, human resources, and technologies. To encourage the digitization process, we present a guideline that offers low-cost and technical knowledge solutions yet balances the quality of the work and outcomes. The guideline describes three phases of digitization, namely preproduction, production, and postproduction. The preproduction phase includes human resource planning and selecting the highest priority collections for digitization. In the preproduction phase, a worksheet is provided for the digitizer to document the metadata, as well as a list of equipment needed to set up a digitizer station to image the specimens and associated labels. In the production phase, we place special emphasis on the light and color calibrations, as well as the guidelines for ISO/shutter speed/aperture to ensure a satisfactory quality of the digitized output. Once the specimen and labels have been imaged in the production phase, we demonstrate an end-to-end pipeline that uses optical character recognition (OCR) to transfer the physical text on the labels into a digital form and document it in a worksheet cell. A nationwide capacity workshop is then conducted to impart the guideline, and pre- and postcourse surveys were conducted to assess the confidence and skills acquired by the participants. This paper also discusses the challenges and future work that need to be taken forward for proper digital biodiversity data management.
Distance and density dependence in two native Bornean dipterocarp species

Malik N, Edwards D, Freckleton RP

Ecol Evol, 2023 Apr;13(4):e10004.
PMID: 37091565 DOI: 10.1002/ece3.10004

The Janzen-Connell hypothesis proposes that density and distance-dependent mortality generated by specialist natural enemies prevent competitive dominance. Much literature on Janzen-Connell mechanisms comes from the neotropics, and evidence of the role of distance and density-dependence is still relatively sparse. We tested the predictions of the Janzen-Connell hypothesis in a South-East Asian system dominated by mast fruiting species. We hypothesized that seedling survival would decrease with distance and density, seedling growth would increase, and herbivory would decrease, according to the predictions of the Janzen-Connell hypothesis. Experiments were conducted to determine the strength of the Janzen-Connell mechanism by manipulating the density and identity of tree species as a function of the distance from parent trees. Survival of conspecific seedlings was reduced near adult trees of one species, but not another. High densities of seedlings decreased the growth of conspecific seedlings of both species. In both species, herbivory rates decreased with distance in low-density areas. This study indicates that dipterocarp species experienced weak Janzen-Connell effects of distance and density dependence at the growth stage studied. Future studies in this system might focus on earlier life-history stages such as seeds and small seedlings, as well as studying mortality during mast-seeding events.
Fulltext Seagrass-associated fungal communities show distance decay of similarity that has implications for seagrass management and restoration

Wainwright BJ, Zahn GL, Zushi J, Lee NLY, Ooi JLS, Lee JN, et al.

Ecol Evol, 2019 Oct;9(19):11288-11297.
PMID: 31641473 DOI: 10.1002/ece3.5631

Marine fungal biodiversity remains vastly understudied, and even less is known of their biogeography and the processes responsible for driving these distributions in marine environments. We investigated the fungal communities associated with the seagrass Enhalus acoroides collected from Singapore and Peninsular Malaysia to test the hypothesis that fungal communities are homogeneous throughout the study area. Seagrass samples were separated into different structures (leaves, roots, and rhizomes), and a sediment sample was collected next to each plant. Amplicon sequencing of the fungal internal transcribed spacer 1 and subsequent analysis revealed significant differences in fungal communities collected from different locations and different structures. We show a significant pattern of distance decay, with samples collected close to each other having more similar fungal communities in comparison with those that are more distant, indicating dispersal limitations and/or differences in habitat type are contributing to the observed biogeographic patterns. These results add to our understanding of the seagrass ecosystem in an understudied region of the world that is also the global epicenter of seagrass diversity. This work has implications for seagrass management and conservation initiatives, and we recommend that fungal community composition be a consideration for any seagrass transplant or restoration programme.
Detection rates and diel activity patterns of four understudied felids from Borneo

Allen ML, Allan ATL

Ecol Evol, 2024 Sep;14(9):e70301.
PMID: 39279787 DOI: 10.1002/ece3.70301

Carnivore guilds are charismatic and have vital and irreplaceable roles in their native ecosystems, yet many of these species are threatened and remain understudied. Borneo is a biodiversity hotspot that hosts a rich diversity of endemic wildlife but is threatened by deforestation and habitat loss. Using cameras placed by the Smithsonian Institution in Sabah, Borneo, we assessed the detection rates and diel activity patterns of the native felid species. Across 51 camera trap sites between 2016 and 2019, felids were detected 55 times across a combined 9958 trap nights, including 20 independent detection events for Sunda leopard cats, 15 for Sunda clouded leopards, 12 for Borneo bay cats, and 5 for marbled cats, with no detections of flat-headed cats. Collectively, this demonstrates the challenge of sampling cryptic species that have declined due to habitat loss and conflict with humans. Despite this, we show that Borneo bay cats and marbled cats exhibited different diel activity patterns than Sunda cloud leopards, suggesting the smaller species use temporal displacement to avoid competition and predation. Sunda leopard cats exhibited broadly similar activity patterns to Sunda clouded leopard, potentially because the two species typically occupy different dietary and habitat niches. These results demonstrate the importance of devoting future research towards monitoring these species and understanding the mechanisms by which they co-exist.
Fulltext How do terrestrial wildlife communities respond to small-scale Acacia plantations embedded in harvested tropical forest?

Wong ST, Guharajan R, Petrus A, Jubili J, Lietz R, Abrams JF, et al.

Ecol Evol, 2022 Sep;12(9):e9337.
PMID: 36188514 DOI: 10.1002/ece3.9337

To offset the declining timber supply by shifting towards more sustainable forestry practices, industrial tree plantations are expanding in tropical production forests. The conversion of natural forests to tree plantation is generally associated with loss of biodiversity and shifts towards more generalist and disturbance tolerant communities, but effects of mixed-landuse landscapes integrating natural and plantation forests remain little understood. Using camera traps, we surveyed the medium-to-large bodied terrestrial wildlife community across two mixed-landuse forest management areas in Sarawak, Malaysia Borneo which include areas dedicated to logging of natural forests and adjacent planted Acacia forests. We analyzed data from a 25-wildlife species community using a Bayesian community occupancy model to assess species richness and species-specific occurrence responses to Acacia plantations at a broad scale, and to remote-sensed local habitat conditions within the different forest landuse types. All species were estimated to occur in both landuse types, but species-level percent area occupied and predicted average local species richness were slightly higher in the natural forest management areas compared to licensed planted forest management areas. Similarly, occupancy-based species diversity profiles and defaunation indices for both a full community and only threatened and endemic species suggested the diversity and occurrence were slightly higher in the natural forest management areas. At the local scale, forest quality was the most prominent predictor of species occurrence. These associations with forest quality varied among species but were predominantly positive. Our results highlight the ability of a mixed-landuse landscape with small-scale Acacia plantations embedded in natural forests to retain terrestrial wildlife communities while providing an alternate source of timber. Nonetheless, there was a tendency towards reduced biodiversity in planted forests, which would likely be more pronounced in plantations that are larger or embedded in a less natural matrix.
Fulltext Feeding ecology of Ellochelon vaigiensis (Quoy & Gaimard, 1825) living in the Mekong Delta, Vietnam

Dinh QM, Truong NT, Nguyen THD, Lam TTH, Nguyen TTK, Le DQ, et al.

Ecol Evol, 2022 Sep;12(9):e9352.
PMID: 36188496 DOI: 10.1002/ece3.9352

Ellochelon vaigiensis (squaretail mullet) adapts to a wide salt spectrum, grows quickly and is easy to raise with other species, so it is the object of attention in aquaculture. Information on the biology and ecology of the species, diet, in particular, is still scattered. Here, we explore the feeding habit, feeding intensity, and food composition of the squaretail mullet. A total of 942 fish (526 males and 416 females) were collected from November 2020 to October 2021 at four coastal sites in the Mekong Delta, Vietnam. The squaretail mullet is an algi-omnivorous fish, as their relative gut length (1.81) falls into the range 1-3, and the diet is mostly based on algae. The feeding intensity is high due to the high value of the fullness index (4.39 ± 0.08%). The fullness index did not vary by sampling site and month, while RGL and FI changed depending on sex. Bacillariophyta (49.13%), detritus derived from organic matter (30.37%), and Cyanophyta (18.39%) are the dominant food items in the diet composition of E. vaigiensis, in which detritus is the most important food with the highest IRI index. Besides, Euglenophyta (1.00%), Chlorophyta (0.95%), Paramecium (0.06%), Copepoda (0.04%), Rotatoria (0.03%), Polychaeta (0.02%), and Cladocera (0.01%) are also recorded and ranked based on their biovolume. Some differences in diet composition are observed between immature and mature at different seasons and their interactions. Our results increase the knowledge about the feeding ecology of squaretail mullet and can help the sustainable management of this commercially important fish species.
Fulltext Sexual size dimorphism and male reproductive traits vary across populations of a tropical rainforest dung beetle species (Onthophagus babirussa)

Toh KX, Yap S, Goh TG, Puniamoorthy N

Ecol Evol, 2022 Sep;12(9):e9279.
PMID: 36177114 DOI: 10.1002/ece3.9279

Sexual size dimorphism (SSD) arises when natural selection and sexual selection act differently on males and females. Male-biased SSD is rarer in insects and usually indicates strong sexual selection pressure on male body size in a species. Patterns of SSD can also vary between populations of species that are exposed to different environmental conditions, such as differing resource availability and diversity. Here, we investigate intraspecific variation in SSD as well as relative investment in precopulatory (horn length) and postcopulatory traits (sperm length and testes weight) in a tropical rainforest dung beetle Onthophagus babirussa across Singapore and Peninsular Malaysia. Overall, three out of four populations displayed significant male-biased SSD, and SSD was greater in populations with smaller overall body size. Average male body size was similar across all populations while female body size was significantly smaller in Singapore, suggesting that the pronounced SSD may also be due to stronger sexual selection on male body size in Singapore populations. All populations showed significant investment in horns as a weapon likely used in male-male competition, while postcopulatory traits showed no clear scaling relationship with body size, suggesting a higher priority on precopulatory sexual traits in the mating system of this species.
Fulltext Environmental stress influences Malesian Lamiaceae distributions

Trethowan LA, Arvidsson C, Bramley GLC

Ecol Evol, 2022 Nov;12(11):e9467.
PMID: 36340815 DOI: 10.1002/ece3.9467

Dual effects of spatial distance and environment shape archipelagic floras. In Malesia, there are multiple environmental stressors associated with increasing uplands, drought, and metal-rich ultramafic soils. Here, we examine the contrasting impacts of multifactorial environmental stress and spatial distance upon Lamiaceae species distributions. We used a phylogenetic generalized mixed effects model of species occurrence across Malesia's taxonomic database working group areas from Peninsular Malaysia to New Guinea. Predictor variables were environmental stress, spatial distance between areas and two trait principal component axes responsible for increasing fruit and leaf size and a negative correlation between flower size and plant height. We found that Lamiaceae species with smaller fruits and leaves are more likely to tolerate environmental stress and become widely distributed across megadiverse Malesian islands. How global species distribution and diversification are shaped by multifactorial environmental stress requires further examination.
Fulltext Postmating isolation and evolutionary relationships among Fejervarya species from Lesser Sunda, Indonesia and other Asian countries revealed by crossing experiments and mtDNA Cytb sequence analyses

Hasan M, Kurniawan N, Soewondo A, Nalley WMM, Matsui M, Igawa T, et al.

Ecol Evol, 2022 Oct;12(10):e9436.
PMID: 36284521 DOI: 10.1002/ece3.9436

To evaluate the degree of postmating isolation and the evolutionary relationships among frog species in the genus Fejervarya from Indonesia (Lesser Sunda), Bangladesh, China, and Japan, crossing experiments and molecular phylogenetic analyses were carried out. Crossing experiments revealed that reciprocal hybrids among F. iskandari, F. verruculosa, and F. sp. large type and between F. multistriata and F. kawamurai are viable through metamorphosis, while those between the F. iskandari group and F. limnocharis group were completely or partially inviable at the tadpole stage and those between Southeast Asian and South Asian Fejervarya groups were completely inviable at the embryonic stage. The mature reciprocal hybrids between F. iskandari and F. verruculosa from Lesser Sunda, Indonesia, showed some degree of abnormality in spermatogenesis. In phylogenetic analyses based on mtDNA Cytb sequences, F. iskandari formed a sister clade with F. verruculosa from Lesser Sunda, Indonesia, with 8.1% sequence divergence. F. multistriata from China formed a clade with populations of F. limnocharis in Thailand, Malaysia, and Indonesia (topotype), and these taxa showed sister relationships to F. kawamurai from Japan with 8.9% sequence divergence. Fejervarya sp. small type from Bangladesh formed a clade with the other South Asian members of the Fejervarya group and formed a sister clade with the Southeast Asian Fejervarya group, with 23.1% sequence divergence in the Cytb gene. These results showed that the degree of postmating isolation reflects molecular phylogenetic relationships and that F. iskandari and F. verruculosa from Indonesia (Lesser Sunda) are reproductively isolated by abnormalities in spermatogenesis and show genetic differentiation.
Fulltext Community phylogeny and spatial scale affect phylogenetic diversity metrics in a species-rich rainforest in Borneo

Okuno S, Yin T, Nanami S, Matsuyama S, Kamiya K, Tan S, et al.

Ecol Evol, 2022 Nov;12(11):e9536.
PMID: 36440315 DOI: 10.1002/ece3.9536

Community phylogenetic analysis is an effective approach to understanding the process of community formation. The phylogenetic tree of the species pool is reconstructed in the first step, and the phylogenetic tree obtained in the second step is used to analyze phylogenetic diversity. Sythetic trees have often been used in the construction of phylogenentic trees; however, in tropical rainforests with many closely related species, synthetic trees contain many unresolved nodes, which may affect the results of phylogenetic structure analysis. Here, we constructed a phylogenetic tree using DNA barcode sequences (rbcL, matK, trnH-psbA) for 737 tree species from the rainforests of Borneo, which have a high-species diversity and many closely related species. The phylogenetic tree had fewer polytomies and more branch length variations than the Phylocom synthetic trees. Comparison of community phylogenetic analyses indicated that values of the standardized effect size of mean pairwise distance (SES-MPD) were highly correlated between Phylocom and DNA barcode trees, but less so for the standardized effect size of mean nearest taxon distance (SES-MNTD), suggesting that caution is needed when using synthetic trees for communities containing many congeneric species, especially when using SES-MNTD. Simulation analysis suggested that spatial dependence on phylogenetic diversity is related to the phylogenetic signal of the species' habitat niche and the spatial structure of habitat, indicating the importance of detailed phylogeny in understanding community assembly processes.
Fulltext Chloroplast capture and range extension after hybridization in taro (Colocasia esculenta)

Matthews PJ, Hossain MA, Sookchaloem D, Nguyen VD, Wong SY, Joling J, et al.

Ecol Evol, 2024 Aug;14(8):e70082.
PMID: 39206463 DOI: 10.1002/ece3.70082

Complete chloroplast genomes of 17 samples from six species of Colocasia (Araceae) were sequenced, assembled, and aligned together with two previously reported complete genome sequences from taro (Colocasia esculenta). Analysis provides a well-supported phylogenetic tree for taro and closely-related wild Colocasia species in Southeast Asia. Two chloroplast lineages (CI and CII) form a well-defined haplotype group and are found in cultivated taros known as var. esculenta (dasheen, CI), var. antiquorum (eddoe, CII), and in a widespread, commensal wild form known as var. aquatilis (CI). A third lineage (CIII) is also found in wild taros known as var. aquatilis and in the wild species C. lihengiae, C. formosana, and C. spongifolia. We suggest three different scenarios to explain the grouping of CIII wild taros (C. esculenta) with other wild Colocasia species. Chloroplast lineages CI and CIII in C. esculenta and an unknown parent species may be involved in an as yet undated history of hybridization, chloroplast capture, and range extension. Substantial taxonomic revision may be needed for C. esculenta after further studies of morphological and genetic diversity within the crop, in wild populations, and in closely related wild species. The results also point to the Bengal delta as a region of key interest for future research on the origins of tropical wetland taros.
Fulltext Identification of three Asian otter species (Aonyx cinereus, Lutra sumatrana, and Lutrogale perspicillata) using a novel noninvasive PCR-RFLP analysis

Sharma S, Chee-Yoong W, Kannan A, Rama Rao S, Abdul-Patah P, Ratnayeke S

Ecol Evol, 2022 Dec;12(12):e9585.
PMID: 36518624 DOI: 10.1002/ece3.9585

Four species of otters occur in tropical Asia, and all face multiple threats to their survival. Studies of distribution and population trends of these otter species in Asia, where they occur sympatrically, are complicated by their elusive nature and difficulties with reliable identification of species in field surveys. In Malaysia, only three species, the smooth-coated otter, Asian small-clawed otter, and hairy-nosed otter have been reliably reported as residents. We designed a replicable and cost-efficient PCR-RFLP protocol to identify these three species. Using published reference sequences of mitochondrial regions, we designed and tested three PCR-RFLP protocols on DNA extracted from reference samples and 33 spraints of wild otters collected along the North Central Selangor Coast of Malaysia. We amplified and sequenced two fragments (450 and 200 bp) of the mt D-loop region and a 300-bp fragment of the mt ND4 gene using primer sets TanaD, TanaD-Mod, and OTR-ND4, respectively. Amplification products were digested with restriction enzymes to generate species-specific RFLP profiles. We analyzed the costs of all three protocols and compared these with the costs of sequencing for species identification. Amplification success was highest for the smallest PCR product, with the TanaD-Mod primer amplifying DNA from all 33 spraints. TanaD and OTR-ND4 primers amplified DNA from 60.6% and 63.6% spraints, respectively. PCR products of TanaD-Mod provided the expected species-specific RFLP profile for 32 (97%) of the spraints. PCR products of OTR-ND4 provided the expected RFLP profile for all 21 samples that amplified, but TanaD produced spurious bands and inconsistent RFLP profiles. The OTR-ND4 primer-enzyme protocol was the least expensive (437 USD) for processing 100 samples, followed by TanaD-Mod (455 USD). We suggest the use of both OTR-ND4 and TanaD-Mod protocols that show potential for highly efficient and reliable species identification from noninvasive genetic sampling of three Asian otter species. We expect our novel noninvasive PCR-RFLP analysis methods to facilitate population monitoring, ecological and behavioral studies on otters in tropical and subtropical Asia.

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